Baseline Statistics Outputting Same FDR

[Robert Amezquita]

http://shazam.readthedocs.io/en/version-0.1.8---mutation-profiling-enhancements/vignettes/Baseline-Vignette/#testing-the-difference-in-selection-pdfs-between-groups

Documentation and individual testing revealed FDR is the same despite different p-values; graphs seem to support that FDR's should be different. Attached is object and code to reproduce:

shazam::testBaseline(grouped_1, groupBy = "foxp3")

[thanks to Yisi for the find]

[Julian Zhou]

This is unlikely a bug but rather how FDR is expected to behave.

[Robert Amezquita]

Okay, I trust in the stats (esp since I haven't run through the formulas myself), just seems fishy to that the FDR values are the same across both regions, so looked like something is wrong in the calculation..

[Jason Vander Heiden]

Yeah.

Though, we should check that it's not a tibble indexing issue, where we ending up with only the first value instead of a vector of values being assigned into a column.

[Julian Zhou]

Adjusting for multiple testing is done via p.adjust() with method="fdr", which is an alias for "BH". Numerically identical q-values are not erroneous due to the nature of the Benjamin-Hochberg procedure.

See link before for more details.

https://stats.stackexchange.com/questions/263831/over-represented-values-in-fdr-adjusted-p-values

[Robert Amezquita]

Just tested with a new dataset - not a tibble copying error.